[gmx-users] Protein-ligand contact maps

Justin Lemkul jalemkul at vt.edu
Sun Apr 17 18:11:07 CEST 2016

On 4/17/16 3:58 AM, Patricia Jones wrote:
> Hello Dear Users
> I am using Gromacs 5.0 for protein-ligand simulation. After completing 50
> ns MD following Justin's tutorial, I have used gmx_mdmat for protein
> residue contact matrix. Now, I want to use this command for protein-ligand
> atom contacts. Is this possible using mdmat? or is there any other way
> because I have seen some research groups have given contact maps between
> protein side chain atoms and ligand heavy atoms.

This information can be parsed from the matrix produced by mdmat.  AFAIK there 
is no way to get it directly, but the .xpm is just a text file, so getting a 
sub-matrix from the total matrix is straightforward.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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